Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 35997.10 
• Atom Count: 2398 
• Residue Count: 307 
• Unique protein chains: 3

2C93

thrombin inhibitors

• DOI: 10.2210/pdb2C93/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Hirudo medicinalis, Homo sapiens


• Deposited: 2005-12-09 Released: 2006-07-04 
• Deposition Author(s): Howard, N., Abell, C., Blakemore, W., Carr, R., Chessari, G., Congreve, M., Howard, S., Jhoti, H., Murray, C.W., Seavers, L.C.A., van Montfort, R.L.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Free: 0.242 
• R-Value Work: 0.164 

Literature

Application of Fragment Screening and Fragment Linking to the Discovery of Novel Thrombin Inhibitors

Howard, N., Abell, C., Blakemore, W., Chessari, G., Congreve, M., Howard, S., Jhoti, H., Murray, C.W., Seavers, L.C.A., Van Montfort, R.L.M.

(2006) J.Med.Chem. 49: 1346

• PubMed: 16480269 
• DOI: 10.1021/jm050850v
• Primary Citation of Related Structures:  
  2C90, 2C8Z, 2C8Y, 2C8X, 2C8W


• PubMed Abstract: 
  

The screening of fragments is an alternative approach to high-throughput screening for the identification of leads for therapeutic targets. Fragment hits have been discovered using X-ray crystallographic screening of protein crystals of the serine protease enzyme thrombin. The fragment library was designed to avoid any well-precedented, strongly basic functionality. Screening hits included a novel ligand (3), which binds exclusively to the S2-S4 pocket, in addition to smaller fragments which bind to the S1 pocket. The structure of these protein-ligand complexes are presented. A chemistry strategy to link two such fragments together and to synthesize larger drug-sized compounds resulted in the efficient identification of hybrid inhibitors with nanomolar potency (e.g., 7, IC50 = 3.7 nM). These potent ligands occupy the same area of the active site as previously described peptidic inhibitors, while having very different chemical architecture.

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Organizational Affiliation: 

Astex Therapeutics, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
THROMBIN, LIGHT CHAIN	A	36	Homo sapiens	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens) Go to Gene View: F2 Go to UniProtKB:  P00734

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
THROMBIN HEAVY CHAIN	B	259	Homo sapiens	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens) Go to Gene View: F2 Go to UniProtKB:  P00734

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
HIRUDIN VARIANT-2	I	12	Hirudo medicinalis	Mutation(s): 0
Find proteins for P09945 (Hirudo medicinalis) Go to UniProtKB:  P09945

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NA	B	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
C4M	B	N-[(2R,3S)-3-AMINO-2-HYDROXY-4-PHENYLBUTYL]-4-METHOXY-2,3,6-TRIMETHYLBENZENESULFONAMIDE INHIBITOR OF THROMBIN C20 H28 N2 O4 S HORGTFOBJRCVMO-ZWKOTPCHSA-N
DMS	B	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TYS	I	L-PEPTIDE LINKING	C9 H11 N O6 S		TYR

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
C4M	IC50: 12000 nM (100) BINDINGDB
C4M	IC50: 12000 nM BINDINGMOAD
C4M	IC50: 12000 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Free: 0.242 
• R-Value Work: 0.164 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 70.657	α = 90.00
b = 71.561	β = 100.65
c = 71.960	γ = 90.00

Software Package:

Software Name	Purpose
REFMAC	refinement
IN-HOUSE	phasing
d*TREK	data scaling
d*TREK	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-12-09 
• Released Date: 2006-07-04 
• Deposition Author(s): Howard, N., Abell, C., Blakemore, W., Carr, R., Chessari, G., Congreve, M., Howard, S., Jhoti, H., Murray, C.W., Seavers, L.C.A., van Montfort, R.L.M.

Revision History 

• Version 1.0: 2006-07-04
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.2: 2013-08-07
  Type: Derived calculations, Other
• Version 1.3: 2015-04-15
  Type: Source and taxonomy
• Version 1.4: 2017-06-28
  Type: Data collection